% This file was created with JabRef 2.7b.
% Encoding: UTF-8

@BOOK{bishop,
  title = {{Pattern recognition and machine learning}},
  publisher = {Springer},
  year = {2006},
  author = {Bishop, Christopher M.},
  edition = {1st ed. 2006. Corr. 2nd printing},
  month = oct,
  abstract = {{The field of pattern recognition has undergone substantial development
	over the years. This book reflects these developments while providing
	a grounding in the basic concepts of pattern recognition and machine
	learning. It is aimed at advanced undergraduates or first year PhD
	students, as well as researchers and practitioners.}},
  citeulike-article-id = {873540},
  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp;path=ASIN/0387310738},
  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&amp;path=ASIN/0387310738},
  citeulike-linkout-10 = {http://www.worldcat.org/oclc/71008143},
  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&amp;path=ASIN/0387310738},
  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0387310738},
  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0387310738/citeulike00-21},
  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0387310738},
  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0387310738},
  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0387310738},
  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0387310738\&index=books\&linkCode=qs},
  citeulike-linkout-9 = {http://www.librarything.com/isbn/0387310738},
  comment = {Bible of Machine Learning},
  day = {01},
  howpublished = {Hardcover},
  isbn = {0387310738},
  keywords = {learning, machine},
  owner = {philipp},
  posted-at = {2007-04-19 15:37:27},
  priority = {5},
  timestamp = {2012.08.16},
  url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0387310738}
}

@ARTICLE{Chapman1996153,
  author = {Henry N. Chapman},
  title = {Phase-retrieval X-ray microscopy by Wigner-distribution deconvolution},
  journal = {Ultramicroscopy},
  year = {1996},
  volume = {66},
  pages = {153 - 172},
  number = {3–4},
  doi = {10.1016/S0304-3991(96)00084-8},
  issn = {0304-3991},
  keywords = {07.85.-m},
  owner = {philipp},
  timestamp = {2012.08.15},
  url = {http://www.sciencedirect.com/science/article/pii/S0304399196000848}
}

@ARTICLE{Chapman06,
  author = {Chapman, Henry N. and Barty, Anton and Marchesini, Stefano and Noy,
	Aleksandr and Hau-Riege, Stefan P. and Cui, Congwu and Howells, Malcolm
	R. and Rosen, Rachel and He, Haifeng and Spence, John C. H. and Weierstall,
	Uwe and Beetz, Tobias and Jacobsen, Chris and Shapiro, David},
  title = {{High-resolution ab initio three-dimensional x-ray diffraction microscopy}},
  journal = {J. Opt. Soc. Am. A},
  year = {2006},
  volume = {23},
  pages = {1179--1200},
  number = {5},
  month = may,
  abstract = {{Coherent x-ray diffraction microscopy is a method of imaging nonperiodic
	isolated objects at resolutions limited, in principle, by only the
	wavelength and largest scattering angles recorded. We demonstrate
	x-ray diffraction imaging with high resolution in all three dimensions,
	as determined by a quantitative analysis of the reconstructed volume
	images. These images are retrieved from the three-dimensional diffraction
	data using no a priori knowledge about the shape or composition of
	the object, which has never before been demonstrated on a nonperiodic
	object. We also construct two-dimensional images of thick objects
	with greatly increased depth of focus (without loss of transverse
	spatial resolution). These methods can be used to image biological
	and materials science samples at high resolution with x-ray undulator
	radiation and establishes the techniques to be used in atomic-resolution
	ultrafast imaging at x-ray free-electron laser sources.}},
  citeulike-article-id = {3333512},
  citeulike-linkout-0 = {http://dx.doi.org/10.1364/JOSAA.23.001179},
  citeulike-linkout-1 = {http://www.opticsinfobase.org/abstract.cfm?id=89531},
  day = {1},
  doi = {10.1364/JOSAA.23.001179},
  keywords = {diffraction, phase\_retrieval, x-ray},
  owner = {philipp},
  posted-at = {2011-06-09 01:11:27},
  priority = {2},
  publisher = {OSA},
  timestamp = {2012.08.15},
  url = {http://dx.doi.org/10.1364/JOSAA.23.001179}
}

@ARTICLE{Elser:03,
  author = {Veit Elser},
  title = {Phase retrieval by iterated projections},
  journal = {J. Opt. Soc. Am. A},
  year = {2003},
  volume = {20},
  pages = {40--55},
  number = {1},
  month = {Jan},
  abstract = {Several strategies in phase retrieval are unified by an iterative
	``difference map'' constructed from a pair of elementary projections
	and three real parameters. For the standard application in optics,
	where the two projections implement Fourier modulus and object support
	constraints, respectively, the difference map reproduces the ``hybrid''
	form of Fienup's input--output map when a particular choice is made
	for two of the parameters. The geometric construction of the difference
	map illuminates the distinction between its fixed points and the
	recovered object, as well as the mechanism whereby the form of stagnation
	encountered by alternating projection schemes is avoided. When support
	constraints are replaced by object histogram or atomicity constraints,
	the difference map lends itself to crystallographic phase retrieval.
	Numerical experiments with synthetic data suggest that structures
	with hundreds of atoms can be solved.},
  doi = {10.1364/JOSAA.20.000040},
  keywords = {Phase retrieval},
  owner = {philipp},
  publisher = {OSA},
  timestamp = {2012.08.24},
  url = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-1-40}
}

@ARTICLE{Fienup:82,
  author = {J. R. Fienup},
  title = {Phase retrieval algorithms: a comparison},
  journal = {Appl. Opt.},
  year = {1982},
  volume = {21},
  pages = {2758--2769},
  number = {15},
  month = {Aug},
  abstract = {Iterative algorithms for phase retrieval from intensity data are compared
	to gradient search methods. Both the problem of phase retrieval from
	two intensity measurements (in electron microscopy or wave front
	sensing) and the problem of phase retrieval from a single intensity
	measurement plus a non-negativity constraint (in astronomy) are considered,
	with emphasis on the latter. It is shown that both the error-reduction
	algorithm for the problem of a single intensity measurement and the
	Gerchberg-Saxton algorithm for the problem of two intensity measurements
	converge. The error-reduction algorithm is also shown to be closely
	related to the steepest-descent method. Other algorithms, including
	the input-output algorithm and the conjugate-gradient method, are
	shown to converge in practice much faster than the error-reduction
	algorithm. Examples are shown.},
  doi = {10.1364/AO.21.002758},
  owner = {philipp},
  publisher = {OSA},
  timestamp = {2012.08.24},
  url = {http://ao.osa.org/abstract.cfm?URI=ao-21-15-2758}
}

@ARTICLE{Fienup:78,
  author = {J. R. Fienup},
  title = {Reconstruction of an object from the modulus of its Fourier transform},
  journal = {Opt. Lett.},
  year = {1978},
  volume = {3},
  pages = {27--29},
  number = {1},
  month = {Jul},
  abstract = {We present a digital method for solving the phase-retrieval problem
	of optical-coherence theory: the reconstruction of a general object
	from the modulus of its Fourier transform. This technique should
	be useful for obtaining high-resolution imagery from interferometer
	data.},
  doi = {10.1364/OL.3.000027},
  owner = {philipp},
  publisher = {OSA},
  timestamp = {2012.08.15},
  url = {http://ol.osa.org/abstract.cfm?URI=ol-3-1-27}
}

@ARTICLE{GSalgo,
  author = {Gerchberg, R. W. and Saxton, W. Owen},
  title = {{A practical algorithm for the determination of the phase from image
	and diffraction plane pictures}},
  journal = {Optik},
  year = {1972},
  volume = {35},
  pages = {237--246},
  citeulike-article-id = {6711014},
  keywords = {algorithm, cgh, hologram, pingpong},
  owner = {philipp},
  posted-at = {2010-02-22 12:40:24},
  priority = {2},
  timestamp = {2012.08.15}
}

@ARTICLE{Guizar-Sicairos:08,
  author = {Manuel Guizar-Sicairos and James R. Fienup},
  title = {Phase retrieval with transverse translation diversity: a nonlinearoptimization
	approach},
  journal = {Opt. Express},
  year = {2008},
  volume = {16},
  pages = {7264--7278},
  number = {10},
  month = {May},
  abstract = {We develop and test a nonlinear optimization algorithm for solving
	the problem of phase retrieval with transverse translation diversity,
	where the diverse far-field intensity measurements are taken after
	translating the object relative to a known illumination pattern.
	Analytical expressions for the gradient of a squared-error metric
	with respect to the object, illumination and translations allow joint
	optimization of the object and system parameters. This approach achieves
	superior reconstructions, with respect to a previously reported technique
	\[H. M. L. Faulkner and J. M. Rodenburg, Phys. Rev. Lett. 93, 023903
	(2004)\], when the system parameters are inaccurately known or in
	the presence of noise. Applicabilityof this method for samples that
	are smaller than the illumination pattern isexplored.},
  doi = {10.1364/OE.16.007264},
  keywords = {Image reconstruction techniques; Phase retrieval; X-ray imaging; X-rays,
	soft x-rays, extreme ultraviolet (EUV); Inverse scattering},
  owner = {philipp},
  publisher = {OSA},
  timestamp = {2012.08.15},
  url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-16-10-7264}
}

@ELECTRONIC{luke2004,
  author = {Luke, Russell D.},
  month = may,
  year = {2004},
  title = {{Relaxed Averaged Alternating Reflections for Diffraction Imaging}},
  url = {http://arxiv.org/abs/math.OC/0405208},
  abstract = {{We report on progress in algorithms for iterative phase retrieval.
	The theory of convex optimization is used to develop and to gain
	insight into counterparts for the nonconvex problem of phase retrieval.
	We propose a relaxation of averaged alternating reflectors and determine
	the fixed point set of the related operator in the convex case. A
	numerical study supports our theoretical observations and demonstrates
	the effectiveness of the algorithm compared to the current state
	of the art.}},
  archiveprefix = {arXiv},
  citeulike-article-id = {709303},
  citeulike-linkout-0 = {http://arxiv.org/abs/math.OC/0405208},
  citeulike-linkout-1 = {http://arxiv.org/pdf/math.OC/0405208},
  day = {12},
  eprint = {math.OC/0405208},
  keywords = {phase-retrieval},
  owner = {philipp},
  posted-at = {2006-06-23 22:04:09},
  priority = {2},
  timestamp = {2012.08.24}
}

@BOOK{citeulike:141092,
  title = {{Information theory, inference and learning algorithms}},
  publisher = {Cambridge University Press},
  year = {2007},
  author = {MacKay, David J. C.},
  edition = {First Edition},
  month = oct,
  abstract = {{Information theory and inference, often taught separately, are here
	united in one entertaining textbook. These topics lie at the heart
	of many exciting areas of contemporary science and engineering -
	communication, signal processing, data mining, machine learning,
	pattern recognition, computational neuroscience, bioinformatics,
	and cryptography. This textbook introduces theory in tandem with
	applications. Information theory is taught alongside practical communication
	systems, such as arithmetic coding for data compression and sparse-graph
	codes for error-correction. A toolbox of inference techniques, including
	message-passing algorithms, Monte Carlo methods, and variational
	approximations, are developed alongside applications of these tools
	to clustering, convolutional codes, independent component analysis,
	and neural networks. The final part of the book describes the state
	of the art in error-correcting codes, including low-density parity-check
	codes, turbo codes, and digital fountain codes -- the twenty-first
	century standards for satellite communications, disk drives, and
	data broadcast. Richly illustrated, filled with worked examples and
	over 400 exercises, some with detailed solutions, David MacKay's
	groundbreaking book is ideal for self- learning and for undergraduate
	or graduate courses. Interludes on crosswords, evolution, and sex
	provide entertainment along the way. In sum, this is a textbook on
	information, communication, and coding for a new generation of students,
	and an unparalleled entry point into these subjects for professionals
	in areas as diverse as computational biology, financial engineering,
	and machine learning.}},
  citeulike-article-id = {141092},
  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp;path=ASIN/0521642981},
  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&amp;path=ASIN/0521642981},
  citeulike-linkout-10 = {http://www.worldcat.org/oclc/52377690},
  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&amp;path=ASIN/0521642981},
  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521642981},
  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521642981/citeulike00-21},
  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521642981},
  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521642981},
  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521642981},
  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521642981\&index=books\&linkCode=qs},
  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521642981},
  comment = {This is an excellent book unifying "information theory" and "machine
	learning".
	
	The author is shows great generocity by sharing it online for free:
	http://wol.ra.phy.cam.ac.uk/mackay/itila/book.html
	
	This book is recommended by Neal at his class for baysian inferencing:
	http://www.cs.utoronto.ca/\~{}radford/csc2541/index.html},
  day = {06},
  howpublished = {Hardcover},
  isbn = {0521642981},
  keywords = {baysian, inference, information, theory},
  owner = {philipp},
  posted-at = {2005-04-18 19:52:11},
  priority = {4},
  timestamp = {2012.08.16},
  url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521642981}
}

@ARTICLE{citeulike:3333781,
  author = {Miao, Jianwei and Charalambous, Pambos and Kirz, Janos and Sayre,
	David},
  title = {{Extending the methodology of X-ray crystallography to allow imaging
	of micrometre-sized non-crystalline specimens}},
  journal = {Nature},
  year = {1999},
  volume = {400},
  pages = {342--344},
  number = {6742},
  month = jul,
  abstract = {{The contrast and penetrating power afforded by soft X-rays when they
	interact with matter makes this form of radiation ideal for studying
	micrometre-sized objects1,2. But although soft X-rays areuseful for
	probing detail too fine for visible light microscopy in specimens
	too thick for electron microscopy, the highest-resolution applications
	of X-ray imaging have been traditionally limited to crystalline samples.
	Here we demonstrate imaging (at 75 nm resolution) of a non-crystalline
	sample, consisting of an array of gold dots, by measuring the soft
	X-ray diffraction pattern from which an image can be reconstructed.
	The crystallographic phase problem3 — the usually unavoidable loss
	of phase information in the diffraction intensity — is overcome by
	oversampling4 the diffraction pattern, and the image is obtained
	using an iterative algorithm5. Our X-ray microscopy technique requires
	no high-resolution X-ray optical elements or detectors. We believe
	that resolutions of 10–20 nm should be achievable; this would provide
	an imaging resolution about 100 times lower than that attainable
	with conventional X-ray crystallography, but our method is applicable
	to structures roughly 100 times larger. This latter feature may facilitate
	the imaging of small whole cells or large subcellular structures
	in cell biology.}},
  citeulike-article-id = {3333781},
  citeulike-linkout-0 = {http://dx.doi.org/10.1038/22498},
  citeulike-linkout-1 = {http://dx.doi.org/10.1038/400342a0},
  day = {22},
  doi = {10.1038/22498},
  issn = {0028-0836},
  keywords = {xfel},
  owner = {philipp},
  posted-at = {2008-09-24 20:33:47},
  priority = {2},
  publisher = {Nature Publishing Group},
  timestamp = {2012.08.15},
  url = {http://dx.doi.org/10.1038/22498}
}

@BOOK{Press2007,
  title = {{Numerical Recipes: The Art of Scientific Computing}},
  publisher = {Cambridge University Press},
  year = {2007},
  author = {Press, William H. and Teukolsky, Saul A. and Vetterling, William
	T. and Flannery, Brian P.},
  edition = {3},
  booktitle = {Numerical Recipes: The Art of Scientific Computing},
  citeulike-article-id = {1386464},
  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp;path=ASIN/0521880688},
  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&amp;path=ASIN/0521880688},
  citeulike-linkout-10 = {http://www.worldcat.org/oclc/123285342},
  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&amp;path=ASIN/0521880688},
  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521880688},
  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521880688/citeulike00-21},
  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521880688},
  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521880688},
  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521880688},
  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521880688\&index=books\&linkCode=qs},
  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521880688},
  isbn = {978-0-521-88407-5},
  keywords = {algorithms, c, computing, numerics, simulation},
  owner = {philipp},
  posted-at = {2011-05-02 13:48:48},
  priority = {0},
  timestamp = {2012.08.24},
  url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521880688}
}

@ARTICLE{Shapiro2005,
  author = {Shapiro, David and Thibault, Pierre and Beetz, Tobias and Elser,
	Veit and Howells, Malcolm and Jacobsen, Chris and Kirz, Janos and
	Lima, Enju and Miao, Huijie and Neiman, Aaron M. and Sayre, David},
  title = {{Biological imaging by soft x-ray diffraction microscopy}},
  journal = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {2005},
  volume = {102},
  pages = {15343--15346},
  number = {43},
  month = oct,
  abstract = {{10.1073/pnas.0503305102 We have used the method of x-ray diffraction
	microscopy to image the complex-valued exit wave of an intact and
	unstained yeast cell. The images of the freeze-dried cell, obtained
	by using 750-eV x-rays from different angular orientations, portray
	several of the cell's major internal components to 30-nm resolution.
	The good agreement among the independently recovered structures demonstrates
	the accuracy of the imaging technique. To obtain the best possible
	reconstructions, we have implemented procedures for handling noisy
	and incomplete diffraction data, and we propose a method for determining
	the reconstructed resolution. This work represents a previously uncharacterized
	application of x-ray diffraction microscopy to a specimen of this
	complexity and provides confidence in the feasibility of the ultimate
	goal of imaging biological specimens at 10-nm resolution in three
	dimensions. ER -  }},
  citeulike-article-id = {557078},
  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0503305102},
  citeulike-linkout-1 = {http://www.pnas.org/content/102/43/15343.abstract},
  citeulike-linkout-2 = {http://www.pnas.org/content/102/43/15343.full.pdf},
  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/102/43/15343},
  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16219701},
  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16219701},
  day = {25},
  doi = {10.1073/pnas.0503305102},
  keywords = {diffraction, microscopy, p\_my\_db\_cul, x-ray},
  owner = {philipp},
  pmid = {16219701},
  posted-at = {2010-07-20 04:20:15},
  priority = {2},
  timestamp = {2012.08.20},
  url = {http://dx.doi.org/10.1073/pnas.0503305102}
}

@ARTICLE{citeulike:3211396,
  author = {Thibault, Pierre and Dierolf, Martin and Menzel, Andreas and Bunk,
	Oliver and David, Christian and Pfeiffer, Franz},
  title = {{High-Resolution Scanning X-ray Diffraction Microscopy}},
  journal = {Science},
  year = {2008},
  volume = {321},
  pages = {379--382},
  number = {5887},
  month = jul,
  abstract = {{Coherent diffractive imaging (CDI) and scanning transmission x-ray
	microscopy (STXM) are two popular microscopy techniques that have
	evolved quite independently. CDI promises to reach resolutions below
	10 nanometers, but the reconstruction procedures put stringent requirements
	on data quality and sample preparation. In contrast, STXM features
	straightforward data analysis, but its resolution is limited by the
	spot size on the specimen. We demonstrate a ptychographic imaging
	method that bridges the gap between CDI and STXM by measuring complete
	diffraction patterns at each point of a STXM scan. The high penetration
	power of x-rays in combination with the high spatial resolution will
	allow investigation of a wide range of complex mesoscopic life and
	material science specimens, such as embedded semiconductor devices
	or cellular networks.}},
  citeulike-article-id = {3211396},
  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1158573},
  citeulike-linkout-1 = {http://www.sciencemag.org/content/321/5887/379.abstract},
  citeulike-linkout-2 = {http://www.sciencemag.org/content/321/5887/379.full.pdf},
  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/321/5887/379},
  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18635796},
  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18635796},
  day = {18},
  doi = {10.1126/science.1158573},
  keywords = {diffraction, for\_slides, microscopy, p\_my\_db\_cul, x-ray},
  owner = {philipp},
  pmid = {18635796},
  posted-at = {2009-04-15 08:00:35},
  priority = {2},
  timestamp = {2012.08.15},
  url = {http://dx.doi.org/10.1126/science.1158573}
}

@ARTICLE{thibault2012,
  author = {P Thibault and M Guizar-Sicairos},
  title = {Maximum-likelihood refinement for coherent diffractive imaging},
  journal = {New Journal of Physics},
  year = {2012},
  volume = {14},
  pages = {063004},
  number = {6},
  abstract = {We introduce the application of maximum-likelihood (ML) principles
	to the image reconstruction problem in coherent diffractive imaging.
	We describe an implementation of the optimization procedure for ptychography,
	using conjugate gradients and including preconditioning strategies,
	regularization and typical modifications of the statistical noise
	model. The optimization principle is compared to a difference map
	reconstruction algorithm. With simulated data important improvements
	are observed, as measured by a strong increase in the signal-to-noise
	ratio. Significant gains in resolution and sensitivity are also demonstrated
	in the ML refinement of a reconstruction from experimental x-ray
	data. The immediate consequence of our results is the possible reduction
	of exposure, or dose, by up to an order of magnitude for a reconstruction
	quality similar to iterative algorithms currently in use.},
  owner = {philipp},
  timestamp = {2012.08.17},
  url = {http://stacks.iop.org/1367-2630/14/i=6/a=063004}
}

